Tutorial Part IV - Movement - Solution Exercise 1
Exercise 4
Exercise 4.1
This is recap from Course2. Please plot the animal relocations in two different colours for column ‘daytime’, using the data.frame and one of the options with {ggplot2}, {ggpmap}, {leaflet} or {tmap}. Use the processed file of fox Q (tag5334_gps_proc) and do it in a separate script. Save your script as Course4_Exercise1_*yourname*.R.
Hint: Remember to load the relevant libraries. Note that you might want to plot the locations in the correct spatial dimensions by projecting it using the functions st_as_sf() and st_transform().
- Load the processed data file
library(here)
library(sf)animal <- readRDS(file = here("output", "data-proc", "tag5334_gps_proc.Rds"))
## transform into spatial simple feature sf object
mydf_sf <- st_as_sf(x = animal, ## data.frame(animal) -> bei mir geht's auch ohne data.frame()
coords = c("longitude", "latitude"),
crs = 4326,
sf_column_name = "geometry" )
## and project
mydf_sf_trans <- st_transform(mydf_sf, 5631) ## EPSG-code Pulkovo- Plot the data
Base R
A quick plot from the simple data.frame
## latitude is y-Axis, longitude = x-axis in cartesian coordinate system
plot(animal$latitude ~ animal$longitude,
pch = ".",
col = as.numeric(animal$daytime) + 1) ## + 1 because color 0 is transparent
A quick plot of the movement path, using only the first 50 observations:
plot(animal$latitude[1:50] ~ animal$longitude[1:50], type= 'l') 
The problem: all of the observations are not projected but use the Cartesian coordinates (i.e. in a default, rectangular 2-D projection).
{ggplot2}
The first approach might be to plot the x and y coordinates with using geom_point():
library(ggplot2)
baseplot_df <-
ggplot(data = animal,
aes(x = longitude,
y = latitude,
color = daytime)) +
geom_point(size = 0.01, alpha = 0.5) +
labs(x = "Longitude", y = "Latitude",
title = "Telemetry data") +
theme_bw(base_size = 16)
baseplot_df
Note that the baseplot_df uses x and y coordinates but not the projection (i.e. the distance between points changes when changing the aspect ratio of the plot) as it uses a Cartesian coordinate system as in the base plot.
As we are dealing with spatial data, it is better to use the projected sf object with the dedicated geom_sf() layer for {ggplot2}:
baseplot_sf <-
ggplot(data = mydf_sf_trans,
aes(color = daytime)) +
geom_sf(size = 0.01, alpha = 0.5) +
labs(x = "Longitude", y = "Latitude",
title = "Telemetry data") +
theme_bw(base_size = 16)
baseplot_sf
Get more inspiration here: https://github.com/Z3tt/TidyTuesday/blob/master/R/2020_26_CaribouLocations.Rmd
{ggmap}
We can also add a background using the {ggmap} package. Check the cheatsheet for a quick start to {ggmap}: https://www.nceas.ucsb.edu/sites/default/files/2020-04/ggmapCheatsheet.pdf
library(ggmap)
## define a bounding box for the plot
b <- c(13.460, 52.485, 13.490, 52.500) ## make large enough to plot all data!
my_tiles <- get_map(location = b, maptype = "terrain", source = "osm", zoom = 15)
ggmap(my_tiles) +
geom_point(aes(x = longitude, y = latitude),
data = data.frame(animal),
colour = as.numeric(animal$daytime) + 6,
size = 0.05) +
labs(x = "Latitude", y = "Longitude", title = "Telemetry locations")
{leaflet}
A nice interactive plot can be created with {leaflet}. The first location of the track is marked:
library(leaflet)
# get first location of track
base_wgs84_x <- animal$longitude[1]
base_wgs84_y <- animal$latitude[1]
m_leaf <- leaflet(animal) %>%
addTiles() %>%
addMarkers(lng = base_wgs84_x, lat = base_wgs84_y,
popup = "Start") %>%
addPopups(base_wgs84_x, base_wgs84_y, "Starting point",
options = popupOptions(closeButton = TRUE)) %>%
addCircles(lng = ~longitude, lat = ~latitude, ~5,
stroke = TRUE,
color = "white",
weight = 1,
fill = TRUE,
fillColor = "blue",
fillOpacity = 0.3)
m_leaf{leaflet} maps are great for interactive usage but bad for export -> create maps with {ggplot2} and {ggmap} or {tmap} instead!
{tmap}
Finally a static and an interactive map via {tmap}:
library(tmap)
tmap_mode(mode = "plot")
tm_shape(shp = mydf_sf_trans) +
tm_dots(size = 0.01,
col = "daytime",
alpha = 0.5) 
tmap_mode(mode = "view")
tm_shape(shp = mydf_sf_trans) +
tm_dots(size = 0.01,
col = "daytime",
alpha = 0.5) END
Session Info
Sys.time()## [1] "2022-03-07 10:48:02 CET"sessionInfo()## R version 4.1.2 (2021-11-01)
## Platform: x86_64-w64-mingw32/x64 (64-bit)
## Running under: Windows 10 x64 (build 19043)
##
## Matrix products: default
##
## locale:
## [1] LC_COLLATE=German_Germany.1252 LC_CTYPE=German_Germany.1252
## [3] LC_MONETARY=German_Germany.1252 LC_NUMERIC=C
## [5] LC_TIME=C
## system code page: 65001
##
## attached base packages:
## [1] stats graphics grDevices utils datasets methods base
##
## other attached packages:
## [1] tmap_3.3-2 leaflet_2.0.4.1 ggmap_3.0.0 ggplot2_3.3.5
## [5] sf_1.0-5 here_1.0.1
##
## loaded via a namespace (and not attached):
## [1] bitops_1.0-7 RColorBrewer_1.1-2 httr_1.4.2
## [4] rprojroot_2.0.2 tools_4.1.2 bslib_0.3.1
## [7] utf8_1.2.2 R6_2.5.1 KernSmooth_2.23-20
## [10] DBI_1.1.2 colorspace_2.0-2 raster_3.5-11
## [13] withr_2.4.3 sp_1.4-6 tidyselect_1.1.1
## [16] curl_4.3.2 compiler_4.1.2 leafem_0.1.6
## [19] textshaping_0.3.6 isoband_0.2.5 labeling_0.4.2
## [22] bookdown_0.24 sass_0.4.0 scales_1.1.1
## [25] classInt_0.4-3 proxy_0.4-26 systemfonts_1.0.3
## [28] stringr_1.4.0 digest_0.6.29 rmarkdown_2.11
## [31] base64enc_0.1-3 dichromat_2.0-0 jpeg_0.1-9
## [34] pkgconfig_2.0.3 htmltools_0.5.2 fastmap_1.1.0
## [37] highr_0.9 htmlwidgets_1.5.4 rlang_0.4.12
## [40] jquerylib_0.1.4 farver_2.1.0 generics_0.1.1
## [43] jsonlite_1.7.2 crosstalk_1.2.0 dplyr_1.0.7
## [46] magrittr_2.0.1 s2_1.0.7 Rcpp_1.0.7
## [49] munsell_0.5.0 fansi_0.5.0 abind_1.4-5
## [52] lifecycle_1.0.1 terra_1.4-22 stringi_1.7.5
## [55] leafsync_0.1.0 yaml_2.2.1 MASS_7.3-54
## [58] tmaptools_3.1-1 plyr_1.8.6 grid_4.1.2
## [61] parallel_4.1.2 crayon_1.4.2 lattice_0.20-45
## [64] stars_0.5-5 knitr_1.36 pillar_1.6.4
## [67] rjson_0.2.21 codetools_0.2-18 wk_0.6.0
## [70] XML_3.99-0.8 glue_1.4.2 evaluate_0.14
## [73] leaflet.providers_1.9.0 png_0.1-7 vctrs_0.3.8
## [76] rmdformats_1.0.3 RgoogleMaps_1.4.5.3 gtable_0.3.0
## [79] purrr_0.3.4 tidyr_1.1.4 assertthat_0.2.1
## [82] xfun_0.27 lwgeom_0.2-8 e1071_1.7-9
## [85] ragg_1.1.3 class_7.3-19 viridisLite_0.4.0
## [88] tibble_3.1.6 units_0.7-2 ellipsis_0.3.2